@Chiromom 

RE: There should be some way to just prior to entering it or in set up to indicate (it is not a check). There should be someway to enter an ACH or draft. Any suggestions?

Yes, before you memorize or re-memorize the check, put something like "ACH" in the check number field.  When it's later recorded, it'll still have that value.

Tip:

To update your existing memorized transactions:

- From the memorized transaction list, double-click a transaction to open it.

- Make changes to it, such as putting ACH in the number field.

- Press Ctrl-M to memorize it.

- You'll see a popup message that asks, "Would you like to replace..." (the existing memorized transaction)

- Click the Replace button.

- Then close the transaction window without saving it.